Fig. 1: Structural topology and pairing alignments of the Clivia aptamer.
From: Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift
a, Chemical structure of NBSI. b, Conserved sequence from SELEX screening and predicted secondary structure of the Clivia aptamer. The sequence is color-coded as in d. c, Schematic of the folding topology of the Clivia aptamer based on the tertiary structure. Additional base pairs are formed at the termini of stems P1 and P2. d, Cartoon representation of the tertiary structure of Clivia with ligand NBSI shown in ball representation. NBSI is located at the center of the overall structure and intercalates between two helical segments of the Clivia aptamer. Two fully hydrated Mg2+ (shown in ball representation) were identified between helix P2 and junction J12. e, A11 interacts with the sugar edge of U33 from the minor groove edge of one canonical base pair A4–U33. f, A12 interacts with G5 along its Watson–Crick edge from the minor groove edge of one canonical base pair G5–C32. The 2′-OH group of U10 forms a hydrogen bond with the N7 atom of A12. g, A6 forms a reverse Watson–Crick base pair with A31. A13 interacts with the Hoogsteen edge of A6 along its Watson–Crick edge.
